Mercurial > repos > galaxytrakr > plasmidtrakr
comparison plasmidtrakr.xml @ 0:f25631df0e9f draft
planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
| author | galaxytrakr |
|---|---|
| date | Wed, 29 Apr 2026 15:04:37 +0000 |
| parents | |
| children | fe9ff3859d68 |
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| -1:000000000000 | 0:f25631df0e9f |
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| 1 <tool id="plasmidtrakr" name="Predict Isolate Source" version="0.1.0"> | |
| 2 <description>Predicts isolate source from plasmid profiles using a trained machine learning model</description> | |
| 3 | |
| 4 <requirements> | |
| 5 <requirement type="package" version="1.5.3">pandas</requirement> | |
| 6 <requirement type="package" version="1.2.2">scikit-learn</requirement> | |
| 7 </requirements> | |
| 8 | |
| 9 <!-- FIXED: Added $ before __tool_directory__ --> | |
| 10 <version_command> | |
| 11 python '$__tool_directory__/predict_source.py' --version | |
| 12 </version_command> | |
| 13 | |
| 14 <!-- FIXED: Added $ before __tool_directory__ --> | |
| 15 <command detect_errors="exit_code"><![CDATA[ | |
| 16 python '$__tool_directory__/predict_source.py' | |
| 17 -i '$mash_input' | |
| 18 -b '$model_selection.path' | |
| 19 -t '$threshold' | |
| 20 -o '$prediction_output' | |
| 21 ]]></command> | |
| 22 | |
| 23 <inputs> | |
| 24 <param name="mash_input" type="data" format="tabular" label="Mash Screen Output" help="The tabular output file from the Galaxy 'mash screen' tool."/> | |
| 25 | |
| 26 <param name="model_selection" type="select" label="Select Prediction Model" help="Choose which trained model to use for prediction."> | |
| 27 <options from_data_table="plasmidtrakr_models"> | |
| 28 <validator type="no_options" message="No prediction models are configured. Please contact your Galaxy administrator." /> | |
| 29 </options> | |
| 30 </param> | |
| 31 | |
| 32 <param name="threshold" type="float" value="0.95" label="Mash Identity Threshold" help="Filter plasmid hits below this identity. Must match the threshold used for model training."/> | |
| 33 </inputs> | |
| 34 | |
| 35 <outputs> | |
| 36 <data name="prediction_output" format="tabular" label="Prediction for ${on_string} using ${model_selection.name}" /> | |
| 37 </outputs> | |
| 38 | |
| 39 <!-- FIXED: Cleaned up Markdown formatting in the help block (removed backslashes) --> | |
| 40 <help><![CDATA[ | |
| 41 **What it does** | |
| 42 | |
| 43 This tool takes the list of plasmid hits from the Galaxy **mash screen** tool and uses a pre-trained **machine learning model** to predict the original source of the isolate. | |
| 44 | |
| 45 **Workflow for Genome Assemblies** | |
| 46 | |
| 47 1. Go to the **mash screen** tool in Galaxy. | |
| 48 2. In the **"Single or Paired-end reads"** dropdown, select **"Single"**. | |
| 49 3. For the **"Select fastq dataset"** input, provide your **genome assembly FASTA file**. | |
| 50 4. Run the `mash screen` job against the appropriate plasmid database. | |
| 51 5. Use the tabular output from that job as the input for **this prediction tool**. | |
| 52 6. Select the desired prediction model from the dropdown menu. | |
| 53 7. Execute to get your prediction. | |
| 54 | |
| 55 **Output** | |
| 56 | |
| 57 A tabular file containing the isolate ID, the predicted source, and a confidence score. | |
| 58 ]]></help> | |
| 59 | |
| 60 <citations> | |
| 61 <citation type="bibtex"> | |
| 62 @misc{strain_2026_plasmidtrakr, | |
| 63 author = {Strain, Errol}, | |
| 64 title = {PlasmidTrakr: A tool for predicting isolate source from plasmid profiles}, | |
| 65 year = {2026}, | |
| 66 publisher = {GitHub}, | |
| 67 journal = {GitHub repository}, | |
| 68 howpublished = {\url{https://github.com/estrain/plasmidtrakr}} | |
| 69 } | |
| 70 </citation> | |
| 71 </citations> | |
| 72 </tool> |